I got exactly the same thing happening when I tried using the Sony software to manage collections on my PRS-505. I suspect is something to do with the rebuilding of indexes that the PRS-505 does as soon as you rebuild a card.
The only way I got my collections back was to reformat the card and then re-download all the books to it from Calibre. There may well be an easier way, but that is my experience. I do not know if I could have simply deleted the books rather than re-formatting the card - but reformatting was quicker!
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